QC saga continues.... from bad to worse

I wasn't sure whether I should have this in my previous post as this is a different issue. I still haven't been able to fix the QC issues and as this is an optional control in the kit we're seeing if getting bad QC score still allows us to detect deletion/duplication events. So I've tried it on control samples that have one gene that contains a duplication/deletion, and did these in duplicates. The QCs fail (as expected now), but the array is detecting a mutation event in the gene of interest (GOI), but for some of the samples instead of detecting a dup, the array would call it a del. To top it off.... a lot of GOI for my project is being called to have dels/dups and this is just not believeable to me, we're expecting one or two for each sample. These same "calls" are appearing in many of my samples. Contamination? I've been careful with how I perform the reactions so I'm a bit boggled as to wear the contamination could come from.